test: add tests for to_hashable_items, variant_distance, and split_haplotypes#15
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ameynert wants to merge 1 commit intoam_13_enable_hail_testsfrom
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test: add tests for to_hashable_items, variant_distance, and split_haplotypes#15ameynert wants to merge 1 commit intoam_13_enable_hail_testsfrom
ameynert wants to merge 1 commit intoam_13_enable_hail_testsfrom
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…plotypes Covers the three non-reference-data functions in haplotype.py: - to_hashable_items: empty dict, single entry, sort order - variant_distance: adjacent SNPs (distance 0), SNPs with gap, deletion that closes a gap - split_haplotypes: no split needed, split at large gap, singleton segment discarded The variant_distance and split_haplotypes tests require a Hail context and request the session-scoped hail_context fixture from conftest.py. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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✨ Finishing Touches🧪 Generate unit tests (beta)
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Summary
Adds
tests/test_haplotype.pycovering the three functions inhaplotype.pythat don't require reference genome sequence data:to_hashable_items: empty dict, single entry, sort-by-key ordervariant_distance(requireshail_context): adjacent SNPs (distance 0), SNPs with a gap, deletion that closes the gapsplit_haplotypes(requireshail_context): no split when all variants fit in one window; split at a gap exceeding the window; singleton segment discarded after a splitThe
variant_distanceandsplit_haplotypestests use the session-scopedhail_contextfixture and a_make_haplotype_tablehelper that builds a minimal Hail table with atstructschema (position-only locus, alleles, haplotype, gnomad_freqs).Test plan
pixi run check-allpassestest_haplotype.pypass🤖 Generated with Claude Code